Tests and documentation for derivative module

.gitlab-ci.yml

@@ -130,4 +130,4 @@ pages:
   tags:
     - docker
   only:
-    - master@software/pystencils
+    - master@pycodegen/pystencils

doc/sphinx/tutorials.rst

@@ -15,6 +15,6 @@ It is a good idea to download them and run them directly to be able to play arou
    /notebooks/05_tutorial_phasefield_spinodal_decomposition.ipynb
    /notebooks/06_tutorial_phasefield_dentritic_growth.ipynb
    /notebooks/demo_assignment_collection.ipynb
+   /notebooks/demo_derivatives.ipynb
    /notebooks/demo_benchmark.ipynb
    /notebooks/demo_wave_equation.ipynb
-

pystencils/fd/derivative.py

 import sympy as sp
 from collections import namedtuple, defaultdict
-
 from pystencils import Field
 from pystencils.sympyextensions import normalize_product, prod
 
@@ -214,6 +213,11 @@ def diff_terms(expr):
 
     This function yields different results than 'expr.atoms(Diff)' when nested derivatives are in the expression,
     since this function only returns the outer derivatives
+
+    Example:
+        >>> x, y = sp.symbols("x, y")
+        >>> diff_terms( diff(x, 0, 0)  )
+        {Diff(Diff(x, 0, -1), 0, -1)}
     """
     result = set()
 

pystencils/fd/spatial.py

@@ -11,6 +11,7 @@ from .derivation import FiniteDifferenceStencilDerivation
 
 def fd_stencils_standard(indices, dx, fa):
     order = len(indices)
+    assert all(i >= 0 for i in indices), "Can only discretize objects with (integer) subscripts"
     if order == 1:
         idx = indices[0]
         return (fa.neighbor(idx, 1) - fa.neighbor(idx, -1)) / (2 * dx)
@@ -122,7 +123,6 @@ def discretize_spatial(expr, dx, stencil=fd_stencils_standard):
 
 
 def discretize_spatial_staggered(expr, dx, stencil=fd_stencils_standard):
-
     def staggered_visitor(e, coordinate, sign):
         if isinstance(e, Diff):
             arg, *indices = diff_args(e)

pystencils_tests/test_derivative.py

 import sympy as sp
+import pystencils as ps
 from sympy.printing.latex import LatexPrinter
 from pystencils.fd import *
+from sympy.abc import a, b, t, x, y, z
 
 
 def test_derivative_basic():
-    x, y, z, t = sp.symbols("x y z t")
     d = diff
 
     op1, op2, op3 = DiffOperator(), DiffOperator(target=x), DiffOperator(target=x, superscript=1)
@@ -18,4 +19,31 @@ def test_derivative_basic():
     assert diff_term == dx**2 + 2 * dx * dy + dy**2 + 1
 
     assert DiffOperator.apply(diff_term, t) == d(t, x, x) + 2 * d(t, x, y) + d(t, y, y) + t
+    assert ps.fd.Diff(0) == 0
 
+    expr = ps.fd.diff(ps.fd.diff(x, 0, 0), 1, 1)
+    assert expr.get_arg_recursive() == x
+    assert expr.change_arg_recursive(y).get_arg_recursive() == y
+
+
+def test_derivative_expand_collect():
+    original = Diff(x*y*z)
+    result = combine_diff_products(combine_diff_products(expand_diff_products(original))).expand()
+    assert original == result
+
+    original = -3 * y * z * Diff(x) + 2 * x * z * Diff(y)
+    result = expand_diff_products(combine_diff_products(original)).expand()
+    assert original == result
+
+    original = a + b * Diff(x ** 2 * y * z)
+    expanded = expand_diff_products(original)
+    collect_res = combine_diff_products(combine_diff_products(combine_diff_products(expanded)))
+    assert collect_res == original
+
+
+def test_diff_expand_using_linearity():
+    eps = sp.symbols("epsilon")
+    funcs = [a, b]
+    test = Diff(eps * Diff(a+b))
+    result = expand_diff_linear(test, functions=funcs)
+    assert result == eps * Diff(Diff(a)) + eps * Diff(Diff(b))